BioC 3.5: CHECK report for ALDEx2 on oaxaca

Package: ALDEx2

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.7.0.tar.gz

StartedAt: 2017-03-03 22:56:48 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 22:59:11 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 142.8 seconds

RetCode: 0

Status:  OK

CheckDir: ALDEx2.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ALDEx2.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.7.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ALDEx2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘ALDEx2’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ALDEx2)

name	user	system	elapsed
ALDEx2m-package	0.000	0.000	0.001
aldex	1.272	0.102	1.375
aldex.clr-class	0.171	0.003	0.173
aldex.clr.function-methods	0.048	0.003	0.051
aldex.corr	0.000	0.000	0.001
aldex.effect	2.191	0.013	2.204
aldex.glm	2.796	0.010	2.807
aldex.set.mode	0.057	0.001	0.058
aldex.ttest	0.563	0.004	0.567
getFeatureNames-method	0.053	0.001	0.054
getFeatures-method	0.038	0.001	0.039
getMonteCarloInstances-method	0.043	0.002	0.046
getMonteCarloReplicate-method	0.055	0.003	0.058
getReads-method	0.064	0.002	0.065
getSampleIDs-method	0.043	0.001	0.043
numConditions-method	0.040	0.001	0.041
numFeatures-method	0.051	0.002	0.052
numMCInstances-method	0.043	0.001	0.044
plot.aldex	0.001	0.000	0.000